Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle

(2016) Nathan Cermak et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann et al.   Nature Communications

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

Bacterial evolution: Genomics of metabolic trade-offs

(2016) Martin F. Polz et al.   Nature Microbiology

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Living in the matrix: assembly and control of Vibrio cholerae biofilms

(2015) Jennifer K. Teschler et al.   NATURE REVIEWS MICROBIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Essential genome ofPseudomonas aeruginosain cystic fibrosis sputum

(2015) Keith H. Turner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations

(2014) Y. Yawata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine metaproteomics: deciphering the microbial metabolic food web

(2014) Timothy J. Williams et al.   TRENDS IN MICROBIOLOGY

Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level

(2014) Alison F. Takemura et al.   Frontiers in Microbiology

Mannitol and the Mannitol-Specific Enzyme IIB Subunit Activate Vibrio cholerae Biofilm Formation

(2013) Patrick Ymele-Leki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Vibrio parahaemolyticustype IV pili mediate interactions with diatom-derived chitin and point to an unexplored mechanism of environmental persistence

(2013) Kyle R. Frischkorn et al.   ENVIRONMENTAL MICROBIOLOGY

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

Approaches to querying bacterial genomes with transposon-insertion sequencing

(2013) Lars Barquist et al.   RNA Biology

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

(2012) Gitta Szabo et al.   ISME Journal

The Entner-Doudoroff Pathway Is Obligatory for Gluconate Utilization and Contributes to the Pathogenicity of Vibrio cholerae

(2012) T. Patra et al.   JOURNAL OF BACTERIOLOGY

Marine Microbes See a Sea of Gradients

(2012) R. Stocker   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

(2012) Yanjia J. Zhang et al.   PLoS Pathogens

Positive Regulation of the Vibrio cholerae Porin OmpT by Iron and Fur

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Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Microbial Extracellular Enzymes and the Marine Carbon Cycle

(2010) Carol Arnosti   Annual Review of Marine Science

Metapopulation structure of Vibrionaceae among coastal marine invertebrates

(2010) Sarah P. Preheim et al.   ENVIRONMENTAL MICROBIOLOGY

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

(2010) Jonathan Kennedy et al.   Marine Drugs

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

(2009) J. D. Gawronski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE